A minimal bash script to classify reads using Kraken2

kraken-batch.sh

#!/bin/bash

# Process a directory of paired end reads and classify
# it with kraken2

DATABASE=/data/db/kraken2/standard-16gb/
INPUTDIR=~/kraken-ws/filt/
OUTDIR=${INPUTDIR/filt/kraken2}
THREADS=8

set -euo pipefail

mkdir -p $OUTDIR
for R1 in ${INPUTDIR}/*_R1*gz;
do
        R2=${R1/_R1/_R2};
        BASE=$(basename $R1 | cut -f1 -d_)
        if [ ! -e "$R2" ]; then
          echo "R2 for sample $R1 was not found"
          exit
        fi

        kraken2 --db $DATABASE --threads $THREADS --paired --report $OUTDIR/$BASE.report $R1 $R2 > $OUTDIR/$BASE.tsv
done